Tag: Footprint Analysis

SAFA 1.1 – Semi Automated Footprinting Analysis

SAFA 1.1

:: DESCRIPTION

SAFA (Semi-Automated Footprinting Analysis) is a softwre for rapidly quantifying the band intensities from nucleic acid chemical mapping gels at single nucleotide resolution.The protocols implemented in SAFA have five steps: 1.) Lane identification, 2.) Gel rectification, 3.) Band assignment, 4.) Model fitting, and 5.) Band intensity normalization. SAFA enables the rapid quantitation of gel images containing thousands of discrete bands, thereby eliminating a bottleneck to the analysis of chemical mapping experiments. An experienced user of the software can quantify a gel image in approximately 15 minutes. Although SAFA was developed to analyze hydroxyl radical (·OH) footprints, it effectively quantifies the gel images obtained with other types of chemical mapping probes. We also present a series of tutorial movies that illustrate the best practices and different steps in the SAFA analysis as a supplement to this protocol.

::DEVELOPER

SAFA Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/Windows/MacOsX

:: DOWNLOAD

 SAFA

:: MORE INFORMATION

Citation

Laederach, A., Das, R., Vicens, Q., Pearlman, S.M., Brenowitz, M., Herschlag, D., and Altman, R.B. (2008)
Semi-automated and rapid quantification of nucleic acid footprinting and structure mapping experiment.
Nature Protocols 3(9), 1395-1401. (2008)

CAFA 0.41 – Capillary Automated Footprinting Analysis

CAFA 0.41

:: DESCRIPTION

CAFA is Capillary Automated Footprinting Analysis algorithms. The use of capillary electrophoresis with fluorescently labeled nucleic acids revolutionized DNA sequencing, effectively fueling the genomic revolution. We present an application of this technology for the high-throughput structural analysis of nucleic acids by chemical and enzymatic mapping (‘footprinting’). We achieve the throughput and data quality necessary for genomic-scale structural analysis by combining fluorophore labeling of nucleic acids with novel quantitation algorithms.The accuracy, throughput and reproducibility of CAFA analysis are demonstrated using hydroxyl radical footprinting of RNA. The versatility of CAFA is illustrated by dimethyl sulfate mapping of RNA secondary structure and DNase I mapping of a protein binding to a specific sequence of DNA. Our experimental and computational approach facilitates the acquisition of high-throughput chemical probing data for solution structural analysis of nucleic acids.

::DEVELOPER

CAFA Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/Windows/MacOsX

:: DOWNLOAD

 CAFA

:: MORE INFORMATION

Citation

Mitra S, Shcherbakova IV, Altman RB, Brenowitz M, Laederach A,
High-throughput single-nucleotide structural mapping by capillary automated footprinting analysis,
Nucleic Acids Res. 2008 Jun;36(11):e63. Epub 2008 May 13 (2008)